chrisamiller

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  • Chris Miller
  • http://www.chrismiller.science/
  • chrisamiller@gmail.com
  • 75
  • 9
  • 63

C

bam-window code for getting depth in genomic intervals

biscuit

0 0
C tools for analyzing sodium bisulfite converted sequencing data

kallisto

0 0
Near-optimal RNA-Seq quantification

C++

telseq

0 0
A software for calculating telomere length

Common Workflow Language

MGI's Analysis Workflows and Pipelines managed by the BGA group.
MGI's CWL Cancer Pipelines.

Dockerfile

Basic docker image for ad-hoc genomic analyses
dockerfile for bamsurgeon
a fat pipeline for running WGBS analysis
finger command
docker image for running the gdc client
docker image for https://github.com/aryeelab/guideseq
Image for github.com/chrisamiller/guideseq
docker container for hmMHC - https://github.com/artyomovlab/hmmhc
fork of the quay.io homer image, moving annotations to my hardcoded link
dockerization of phlat hla typing tool
docker image for R synapser package

HTML

cv

0 0
CV webpage

JavaScript

regexbot

0 0
Slackbot for responding to messages that match regexes

Perl

rtm-cli

8 2
A command-line Remember the Milk client written in perl
Short snippets of code useful for bioinformatics and genomics
Convert ensembl GTF from [1,2,3] nomenclature to [chr1, chr2, chr3] nomenclature
Docker containerization for the CLE

genome

0 0
Core modules used by the GMS
Allows programmatic retrieval of peptide cleavage predictions from the NetChop server at http://www.cbs.dtu.dk/services/NetChop/

Python

tools for single-cell RNAseq analysis
Docker container for demultiplexing haloplex data, thanks to ED and HA
tools for single-cell RNAseq analysis, incl seurat
Container for the somatic-llr filter

guideseq

0 0
Analysis pipeline for the GUIDE-seq assay. For news, see:

intervene

0 0
Intervene: a tool for intersection and visualization of multiple genomic region and gene sets

OptiType

0 0
Precision HLA typing from next-generation sequencing data
A tool to design highly specific PCR primers for the validation of genomic alterations including structural variants
A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
A set of tools to annotate VCF files with expression and readcount data

R

fishplot

103 32
Create timecourse "fish plots" that show changes in the clonal architecture of tumors

readDepth

23 10
R package for inferring copy number from read depth

copyCat

15 7
a parallel R package for detecting copy-number alterations from short sequencing reads
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
BioPharma projects

CONICS

0 0
CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
docker image for doing bsseq analysis in R
docker image for the R copyCat package
A fat docker image for running RnaSeq

Ruby

calculate drive times from multiple locations and visualize them in google earth

davidapi

3 1
A ruby wrapper for a few of the DAVID API functions for functional gene annotation (http://david.abcc.ncifcrf.gov/)
copies song ratings from iTunes to Guaydeque music player

RMEmod

1 2
A tool for discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

Shell

Create static screenshots of genomic regions using IGV.